The only way in which 'practically the best possible' holds true, and thereby the only reason to put Vingegaard above/at the same level as Van der Poel, is if you a) value Tour-Vuelta equal to Giro-Tour (I'll return to that later) and b) treat this Vuelta as amounting to a victory. But b) just isn't how that works. History doesn't care about how you got second, history cares about the fact that you didn't win, and does so by largely ignoring your second place (unless you're Poulidor or Fignon). I can see an argument for valuing Vingegaard's second place more highly than most other second places, but it just isn't a win, and without the GT double it is by definition not the best possible stage race season. I also don't think the Itzulia and Dauphiné wins against weak opposition matter too much (nobody will remember this season for those), especially when Pogacar walloped him in Paris-Nice which kind of shatters the aura of perfection.Vingegaard has practically had the best possible stage race season with only 1 big win, MvdP on the other hand only has his three big wins and a 2nd place in Ronde.
Meanwhile, Van der Poel is one place in Ronde away from practically the best classics season possible. In fact, had he pulled it off, it would have been the best non-Merckx classics season ever. If Vingegaard had pulled off the Vuelta win, it would still have fallen well short of Coppi and Roche too as far as GT doubles are concerned. Not to mention that the Giro+Tour double is IMO clearly harder than the Tour+Vuelta double, so you could argue that Hinault, Indurain and Pantani all beat him too. In fact, I would argue that you need the Giro+Tour double for the perfect stage racing season... which means Vingegaard was only on course for the second-best possible stage racing season - and missed. Not as impressive. Heck, Froome would have done Tour+Vuelta+Dauphiné in 2016 without the Formigal ambush, and I don't remember anyone talking about him missing out on a near-perfect stage racing season. Does Itzulia really make that much of a difference compared to that season?
Finally, Van der Poel got three-quarters of the way to his perfect season in terms of big wins, whereas Vingegaard only got halfway. That also matters a lot. Yes, Vingegaard can't get to any sort of quarters, but does that mean that Van der Poel winning three big one-day races rather than two should count for nothing? It's just a lot easier to be one big win away from the perfect stage racing season than it is to be one big win away from the perfect classics season, simply because you only need to land one big win for the former.